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1.
Front Public Health ; 8: 574111, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33324597

RESUMEN

Non-communicable diseases (NCDs) are of increasing concern for society and national governments, as well as globally due to their high mortality rate. The main risk factors of NCDs can be classified into the categories of self-management, genetic factors, environmental factors, factors of medical conditions, and socio-demographic factors. The main focus is on the elements of self-management and to reach a consensus about the influence of food on risk management and actions toward the prevention of NCDs at all stages of life. Nutrition interventions are essential in managing the risk of NCDs. As they are of the utmost importance, this review highlights NCDs and their risk factors and outlines several common prevention strategies. We foresee that the best prevention management strategy will include individual (lifestyle management), societal (awareness management), national (health policy decisions), and global (health strategy) elements, with target actions, such as multi-sectoral partnership, knowledge and information management, and innovations. The most effective preventative strategy is the one that leads to changes in lifestyle with respect to diet, physical activities, cessation of smoking, and the control of metabolic disorders.


Asunto(s)
Enfermedades no Transmisibles , Dieta , Política de Salud , Humanos , Estilo de Vida , Enfermedades no Transmisibles/epidemiología , Factores de Riesgo
2.
Biomolecules ; 9(12)2019 12 17.
Artículo en Inglés | MEDLINE | ID: mdl-31861140

RESUMEN

Recently more consideration has been given to the use of renewable materials and agricultural residues. Wheat production is increasing yearly and correspondingly, the volume of by-products from the wheat process is increasing, as well. It is important to find the use of the residuals for higher value-added products, and not just for the food industry or animal feed purposes as it is happening now. Agricultural residue of the roller milled wheat grain is a wheat bran description. The low-cost of wheat bran and its composition assortment provides a good source of substrate for various enzymes and organic acids production and other biotechnological applications. The main purpose of this review article is to look into recent trends, developments, and applications of wheat bran.


Asunto(s)
Fibras de la Dieta , Animales , Biotecnología , Fibras de la Dieta/economía , Fibras de la Dieta/metabolismo , Fibras de la Dieta/uso terapéutico , Humanos
3.
BMC Res Notes ; 12(1): 720, 2019 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-31675990

RESUMEN

OBJECTIVE: We aim to directly detect Mycoplasma DNA in a U937 suspension cell culture without using DNA purification. In order to make Mycoplasma contamination monitoring easier, we optimized a commercially available quantitative PCR (qPCR)-based detection kit. We compared the sensitivity of direct qPCR against qPCR with a purified DNA template. RESULTS: Our findings indicate that qPCR worked optimally with a 6 µl sample volume and a 52 °C annealing-extension temperature. We were able to decrease the annealing-extension step time from 60 to 20 s without any major decrease in reaction sensitivity. The total cycle time of optimized direct qPCR was 65 min. The optimized qPCR protocol was used to detect Mycoplasma DNA before and after DNA purification. Our findings indicate that direct qPCR had a higher sensitivity than regular qPCR. Ct levels produced by direct qPCR with 6 µl templates were almost identical to Ct levels produced by regular qPCR with DNA purified from a 60 µl cell culture sample (23.42 vs 23.49 average Ct levels, respectively). The optimized direct qPCR protocol was successfully applied to monitor the elimination of Mycoplasma contamination from U937 cell cultures.


Asunto(s)
ADN Bacteriano/genética , ADN Bacteriano/aislamiento & purificación , Mycoplasma/genética , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Humanos , Reproducibilidad de los Resultados , Células U937
4.
BMC Genomics ; 18(1): 450, 2017 06 08.
Artículo en Inglés | MEDLINE | ID: mdl-28595602

RESUMEN

BACKGROUND: Recombinant peptide chips could constitute a versatile complementation to state-of-the-art in situ (chemical on-chip) synthesis, particle-based printing, or pre-manufactured peptide spotting. Bottlenecks still impeding a routine implementation - from restricted peptide lengths, low diversity and low array densities to high costs - could so be overcome. METHODS: To assess overall performance, we assembled recombinant chips composed of 38,400 individual peptide spots on the area of a standard 96-well microtiter plate from comprehensive, highly diverse (>107 single clones) short random peptide libraries. RESULTS: Screening of altogether 476,160 clones against Streptavidin uncovered 2 discrete new binders: a characteristic HPQ-motif containing VSHPQAPF and a cyclic CSGSYGSC peptide. Interactions were technically confirmed by fluorescence polarization as well as biolayer-interferometry, and their potential suitability as novel detection tags evaluated by detection of a peptide-fused exemplary test protein. CONCLUSION: From our data we conclude that the presented technical pipeline can reliably identify novel hits, useful as first-generation binders or templates for subsequent ligand design plus engineering.


Asunto(s)
Biblioteca de Péptidos , Análisis por Matrices de Proteínas/métodos , Proteínas Recombinantes/metabolismo , Ligandos , Estreptavidina/metabolismo
5.
J Virol Methods ; 242: 46-52, 2017 04.
Artículo en Inglés | MEDLINE | ID: mdl-28093274

RESUMEN

Herpes simplex viruses (HSV) are common human pathogens that can cause painful but benign manifestations and recurrent complaints, but can also cause significant morbidity and mortality on infection of the eye or brain and with disseminated infection of an immunosuppressed patient or a neonate. HSV growth inhibition measurement by plaque or yield reduction is a key task in the development of novel antiviral compounds but the manual methods are very labour intensive. The sensitive and specific PCR technology could be an effective method for quantitation of HSV DNA related to virus replication; however the currently described PCR approaches have a major limitation, namely the requirement of purification of DNA from the infected cells. This limitation makes this approach unfeasible for high-throughput screenings. The monitoring of HSV specific antibody titre is essential in vaccination trials and in the improvement of HSV-based oncolytic virotherapy. Usually, conventional cytopathic effect-based and plaque reduction neutralization tests are applied to measure the neutralization titre, but these methods are also time-consuming. To overcome this, we developed a quantitative PCR (qPCR) method for the detection of HSV-2 DNA directly from the infected cells (direct qPCR) and the method was further adapted to measure the titre of HSV specific neutralizing antibody in human sera. The conditions of direct qPCR assay were optimized to measure the antiviral activity of known and novel antiviral substances. Using HSV-2 seronegative and seropositive patients' sera, the validity of the direct qPCR neutralization test was compared to traditional cytopathic effect-based assay. The direct qPCR method was able to detect the HSV-2 DNA quantitatively between multiplicity of infection 1/64 and 1/4194304, indicating that the dynamic range of the detection was approximately 65,500 fold with high correlation between the biological and technical replicates. As a proof of the adaptability of the method, we applied the direct qPCR for antiviral inhibitory concentration 50 (IC50) measurements of known and novel antiviral compounds. The measured IC50 of acyclovir was ∼0.28µg/ml, similar to the previously published IC50 value. The IC50 of novel antiviral candidates was between 1.6-3.1µg/ml. The direct qPCR-based neutralization titres of HSV positive sera were 1:32-1:64, identical to the neutralization titres determined using a traditional neutralization assay. The negative sera did not inhibit the HSV-2 replication in either of the tests. Our direct qPCR method for the HSV-2 growth determination of antiviral IC50 and neutralization titre is less time-consuming, less subjective and a more accurate alternative to the traditional plaque titration and growth reduction assays.


Asunto(s)
Anticuerpos Neutralizantes/sangre , Anticuerpos Antivirales/sangre , Antivirales/farmacología , Herpesvirus Humano 2/efectos de los fármacos , Herpesvirus Humano 2/inmunología , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Aciclovir/farmacología , Genoma Viral , Herpes Simple/inmunología , Herpesvirus Humano 2/genética , Herpesvirus Humano 2/aislamiento & purificación , Humanos , Concentración 50 Inhibidora , Pruebas de Neutralización , Replicación Viral/efectos de los fármacos
6.
Biol Chem ; 398(1): 125-133, 2017 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-27467752

RESUMEN

Acyl-carrier-protein (acpP) is an essential protein in fatty acid biosynthesis of Staphylococcus aureus [Cronan, J.E. and Thomas, J. (2009). Complex enzymes in microbial natural product biosynthesis, part B: polyketides, aminocoumarins and carbohydrates. METHOD: Enzymol. 459, 395-433; Halavaty, A.S., Kim, Y., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Zhou, M., Onopriyenko, O., Skarina, T., Papazisi, L., et al. (2012). Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria. Acta Crystallogr. Sect. D Biol. Crystallogr. 68, 1359-1370]. The inactive apo-form is converted to the active holo-enzyme by acyl-carrier protein synthase (acpS) through addition of a 4'-phosphopantetheine group from coenzyme A to a conserved serine residue of acpP [Flugel, R.S., Hwangbo, Y., Lambalot, R.H., Cronan, J.E., and Walsh, C.T. (2000). Holo-(acyl-carrier protein) synthase and phosphopantetheinyl transfer in Escherichia coli. J. Biol. Chem. 275, 959-968; Lambalot, R.H. and Walsh, C.T. (1995). Cloning, overproduction, and characterization of the Escherichia coli holo-acyl-carrier protein synthase. J. Biol. Chem. 270, 24658-24661]. Once activated, acpP acts as an anchor for the growing fatty acid chain. Structural data from X-ray crystallographic analysis reveals that, despite its small size (8 kDa), acpP adopts a distinct, mostly α-helical structure when complexed with acpS [Halavaty, A.S., Kim, Y., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Zhou, M., Onopriyenko, O., Skarina, T., Papazisi, L., et al. (2012). Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria. Acta Crystallogr. Sect. D Biol. Crystallogr. 68, 1359-1370; Byers, D.M. and Gong, H. (2007). Acyl carrier protein: structure-function relationships in a conserved multifunctional protein family. Biochem. Cell Biol. 85, 649-662]. We expressed and purified recombinant, active S. aureus acpP from Escherichia coli and mimicked the beginning of fatty acid biosynthesis by employing an [14C]-acp loading assay. Surprisingly, acpP remained functional even after heat treatment at 95°C for up to 10 min. NMR data from 2D-HSQC experiments as well as interaction studies with acpS confirmed that acpP is structured and active both before and after heat treatment, with no significant differences between the two. Thus, our data suggest that S. aureus acpP is a highly stable protein capable of maintaining its structure at high temperatures.


Asunto(s)
Proteína Transportadora de Acilo/química , Proteína Transportadora de Acilo/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Staphylococcus aureus , Temperatura , Secuencia de Aminoácidos , Sitios de Unión , Modelos Moleculares , Unión Proteica , Conformación Proteica , Estabilidad Proteica
7.
Oncotarget ; 8(64): 107423-107440, 2017 Dec 08.
Artículo en Inglés | MEDLINE | ID: mdl-29296175

RESUMEN

Complex three-dimensional (3D) in vitro models that recapitulate human tumor biology are essential to understand the pathophysiology of the disease and to aid in the discovery of novel anti-cancer therapies. 3D organotypic cultures exhibit intercellular communication, nutrient and oxygen gradients, and cell polarity that is lacking in two-dimensional (2D) monolayer cultures. In the present study, we demonstrate that 2D and 3D cancer models exhibit different drug sensitivities towards both targeted inhibitors of EGFR signaling and broad acting cytotoxic agents. Changes in the kinase activities of ErbB family members and differential expression of apoptosis- and survival-associated genes before and after drug treatment may account for the differential drug sensitivities. Importantly, EGFR oncoprotein addiction was evident only in the 3D cultures mirroring the effect of EGFR inhibition in the clinic. Furthermore, targeted drug efficacy was strongly increased when incorporating cancer-associated fibroblasts into the 3D cultures. Taken together, we provide conclusive evidence that complex 3D cultures are more predictive of the clinical outcome than their 2D counterparts. In the future, 3D cultures will be instrumental for understanding the mode of action of drugs, identifying genotype-drug response relationships and developing patient-specific and personalized cancer treatments.

8.
Molecules ; 21(10)2016 Sep 27.
Artículo en Inglés | MEDLINE | ID: mdl-27689973

RESUMEN

To design new compounds suitable as starting points for anticancer drug development, we have synthesized a novel series of benzoxazoles with pharmaceutically advantageous piperazine and fluorine moieties attached to them. The newly synthesized benzoxazoles and their corresponding precursors were evaluated for cytotoxicity on human A-549 lung carcinoma cells and non-cancer HepaRG hepatocyes. Some of these new benzoxazoles show potential anticancer activity, while two of the intermediates show lung cancer selective properties at low concentrations where healthy cells are unaffected, indicating a selectivity window for anticancer compounds.

9.
Neuropeptides ; 56: 83-8, 2016 04.
Artículo en Inglés | MEDLINE | ID: mdl-26725588

RESUMEN

Galanin and its receptors (GAL1, GAL2, GAL3) modulate a range of neuronal, immune and vascular activities. In vivo administration of SNAP 37889 (1-phenyl-3-[[3-(trifluoromethyl)phenyl]imino]-1H-indol-2-one), a potent small non-peptidergic antagonist of GAL3, was reported to reduce anxiety- and depression-related behavior, ethanol consumption, and antagonizes the effect of galanin on plasma extravasation in rodent models. Accordingly, SNAP 37889 has been proposed as a potential therapeutic agent to treat anxiety and depression disorders. Therefore, we evaluated the toxicity of SNAP 37889 to different cell types. Our experiments revealed that SNAP 37889 (≥10µM) induced apoptosis in epithelial (HMCB) and microglial (BV-2) cell lines expressing endogenous GAL3, in peripheral blood mononuclear cells and promyelocytic leukemia cells (HL-60) expressing GAL2, and in a neuronal cell line (SH-SY5Y) lacking galanin receptor expression altogether. In conclusion, SNAP 37889 is toxic to a variety of cell types independent of GAL3 expression. We caution that the clinical use of SNAP 37889 at doses that might be used to treat anxiety- or depression- related diseases could have unexpected non-galanin receptor-mediated toxicity, especially on immune cells.


Asunto(s)
Apoptosis/efectos de los fármacos , Indoles/toxicidad , Receptor de Galanina Tipo 3/antagonistas & inhibidores , Animales , Línea Celular , Línea Celular Tumoral , Supervivencia Celular/efectos de los fármacos , Células Epiteliales/efectos de los fármacos , Humanos , Técnicas In Vitro , Leucocitos Mononucleares/efectos de los fármacos , Ratones , Microglía/efectos de los fármacos , Neuronas/efectos de los fármacos
10.
J Microbiol Methods ; 120: 15-22, 2016 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-26578244

RESUMEN

Chlamydiae are obligate intracellular bacteria developing in an intracytoplasmic niche, the inclusion. Chlamydia growth measurement by inclusion counting is a key task in the development of novel antichlamydial antibiotics and in vaccine studies. Most of the current counting methods rely on the immunofluorescent staining of the inclusions and either manual or automatic microscopy detection and enumeration. The manual method is highly labor intensive, while the automatic methods are either medium-throughput or require automatic microscopy. The sensitive and specific PCR technology could be an effective method for growth related chlamydial DNA detection; however the currently described PCR approaches have a major limitation, the requirement of purification of DNA or RNA from the infected cells. This limitation makes this approach unfeasible for high-throughput screenings. To overcome this, we developed a quantitative PCR (qPCR) method for the detection of Chlamydia trachomatis DNA directly from the infected HeLa cells. With our method we were able to detect the bacterial growth in a 4 log scale (multiplicity of infection (MOI): 64 to 0.0039), with high correlation between the biological and technical replicates. As a further proof of the method, we applied the direct qPCR for antibiotic minimum inhibitory concentration (MIC) measurements. The measured MICs of moxifloxacin, tetracycline, clarithromycin and compound PCC00213 were 0.031 µg/ml, 0.031 µg/ml, 0.0039 µg/ml and 6.2 µg/ml respectively, identical or close to the already published MIC values. Our direct qPCR method for chlamydial growth and antibiotic MIC determination is less time-consuming, more objective and more sensitive than the currently applied manual or automatic fluorescent microscopy- based methods.


Asunto(s)
Infecciones por Chlamydia/microbiología , Chlamydia trachomatis/aislamiento & purificación , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Antibacterianos/farmacología , Técnicas Bacteriológicas , Infecciones por Chlamydia/diagnóstico , Infecciones por Chlamydia/genética , Chlamydia trachomatis/efectos de los fármacos , Chlamydia trachomatis/genética , Chlamydia trachomatis/crecimiento & desarrollo , Claritromicina/farmacología , ADN Bacteriano , Células HeLa , Humanos , Pruebas de Sensibilidad Microbiana , ARN Bacteriano , Tetraciclina/farmacología
11.
BMC Res Notes ; 8: 785, 2015 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-26666517

RESUMEN

BACKGROUND: To be able to develop effective therapeutics for epidermolysis bullosa simplex (EBS), it is necessary to elucidate the molecular pathomechanisms that give rise to the disease's characteristic severe skin-blistering phenotype. RESULTS: Starting with a whole-transcriptome microarray analysis of an EBS Dowling-Meara model cell line (KEB7), we identified 207 genes showing differential expression relative to control keratinocytes. A complementary qRT-PCR study of 156 candidates confirmed 76.58 % of the selected genes to be significantly up-regulated or down-regulated (p-value <0.05) within biological replicates. Our hit list contains previously identified genes involved in epithelial cell proliferation, cell-substrate adhesion, and responses to diverse biological stimuli. In addition, we identified novel candidate genes and potential affected pathways not previously considered as relevant to EBS pathology. CONCLUSIONS: Our results broaden our understanding of the molecular processes dysregulated in EBS.


Asunto(s)
Perfilación de la Expresión Génica/métodos , Queratinocitos/metabolismo , Transducción de Señal/genética , Transcriptoma/genética , Western Blotting , Línea Celular , Epidermólisis Ampollosa Simple/tratamiento farmacológico , Epidermólisis Ampollosa Simple/genética , Epidermólisis Ampollosa Simple/patología , Ontología de Genes , Predisposición Genética a la Enfermedad/genética , Humanos , Queratinocitos/efectos de los fármacos , Terapia Molecular Dirigida/métodos , Mutación , Análisis de Secuencia por Matrices de Oligonucleótidos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Transducción de Señal/efectos de los fármacos
12.
Methods Mol Biol ; 1195: 99-109, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24281872

RESUMEN

Cultured human primary keratinocytes constitute suitable targets for in-depth evaluation of the proliferative or differentiative potential of compounds. There is, however, a double-edged and intrinsically inseparable transition from biological activity to cytotoxicity for any agent under investigation. For that reason, we here first of all present an established protocol for the isolation, cultivation, and analysis of primary foreskin-derived keratinocytes. Taking calcitriol as example, we then reveal how a straightforward photometric cell culture assay can be exploited to assess overall cell viability in response to increasing compound doses. With predetermined cellular cytotoxicity at hand, physiologically meaningful (sub-toxic) compound concentrations for subsequent stimulation of cells can be readily selected, and, in doing so, differentially expressed genes with biological significance can be reliably identified.


Asunto(s)
Evaluación Preclínica de Medicamentos/métodos , Perfilación de la Expresión Génica/métodos , Queratinocitos/efectos de los fármacos , Queratinocitos/metabolismo , Calcitriol/farmacología , Calcitriol/toxicidad , Técnicas de Cultivo de Célula , Proliferación Celular/efectos de los fármacos , Separación Celular , Supervivencia Celular/efectos de los fármacos , Criopreservación , Humanos , Queratinocitos/citología , ARN/genética , ARN/aislamiento & purificación , Reacción en Cadena en Tiempo Real de la Polimerasa
13.
Antimicrob Agents Chemother ; 58(1): 405-13, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24189259

RESUMEN

Chlamydiae are obligate intracellular bacteria that propagate in the inclusion, a specific niche inside the host cell. The standard method for counting chlamydiae is immunofluorescent staining and manual counting of chlamydial inclusions. High- or medium-throughput estimation of the reduction in chlamydial inclusions should be the basis of testing antichlamydial compounds and other drugs that positively or negatively influence chlamydial growth, yet low-throughput manual counting is the common approach. To overcome the time-consuming and subjective manual counting, we developed an automatic inclusion-counting system based on a commercially available DNA chip scanner. Fluorescently labeled inclusions are detected by the scanner, and the image is processed by ChlamyCount, a custom plug-in of the ImageJ software environment. ChlamyCount was able to measure the inclusion counts over a 1-log-unit dynamic range with a high correlation to the theoretical counts. ChlamyCount was capable of accurately determining the MICs of the novel antimicrobial compound PCC00213 and the already known antichlamydial antibiotics moxifloxacin and tetracycline. ChlamyCount was also able to measure the chlamydial growth-altering effect of drugs that influence host-bacterium interaction, such as gamma interferon, DEAE-dextran, and cycloheximide. ChlamyCount is an easily adaptable system for testing antichlamydial antimicrobials and other compounds that influence Chlamydia-host interactions.


Asunto(s)
Chlamydia trachomatis/genética , Chlamydia trachomatis/aislamiento & purificación , Chlamydophila pneumoniae/genética , Chlamydophila pneumoniae/aislamiento & purificación , Cuerpos de Inclusión/microbiología , Pruebas de Sensibilidad Microbiana , Análisis de Secuencia por Matrices de Oligonucleótidos
14.
FASEB J ; 27(11): 4476-88, 2013 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-23901070

RESUMEN

Antimicrobial peptides are a promising complement to common antibiotics, development of resistance to which is a growing problem. Here we present a de novo-designed peptide, SP1-1 (RKKRLKLLKRLL-NH2), with antimicrobial activity against multiresistant Staphylococcus aureus (minimal inhibitory concentration: 6.25 µM). Elucidation of the mode of action of this peptide revealed a strong interaction with RsbW kinase (Kd: 6.01±2.73 nM), a serine kinase negatively regulating the activity of the transcription factor σB (SigB). SP1-1 binding and functional modulation of RsbW were shown in vitro by a combination of biochemical, molecular, and biophysical methods, which were further genetically evidenced in vivo by analysis of S. aureus ΔsigB deletion mutants. Intracellular localization of the peptide was demonstrated using nanometer-scaled secondary ion mass spectrometry. Moreover, microarray analysis revealed that transcription of numerous genes, involved in cell wall and amino acid metabolism, transport mechanisms, virulence, and pigmentation, is affected. Interestingly, several WalR binding motif containing genes are induced by SP1-1. In sum, the designed peptide SP1-1 seems to have multiple modes of action, including inhibition of a kinase, and therefore might contribute to the development of new antibacterial compounds, giving bacterial kinase inhibition a closer inspection.


Asunto(s)
Péptidos Catiónicos Antimicrobianos/farmacología , Proteínas Bacterianas/antagonistas & inhibidores , Proteínas Portadoras/antagonistas & inhibidores , Inhibidores de Proteínas Quinasas/farmacología , Proteínas Serina-Treonina Quinasas/antagonistas & inhibidores , Staphylococcus aureus/efectos de los fármacos , Secuencia de Aminoácidos , Péptidos Catiónicos Antimicrobianos/síntesis química , Péptidos Catiónicos Antimicrobianos/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Transporte Biológico/genética , Proteínas Portadoras/genética , Proteínas Portadoras/metabolismo , Relación Dosis-Respuesta a Droga , Datos de Secuencia Molecular , Mutación , Unión Proteica , Inhibidores de Proteínas Quinasas/síntesis química , Proteínas Serina-Treonina Quinasas/genética , Proteínas Serina-Treonina Quinasas/metabolismo , Factor sigma/genética , Factor sigma/metabolismo , Staphylococcus aureus/enzimología , Staphylococcus aureus/genética , Transcripción Genética/efectos de los fármacos , Virulencia/genética
15.
Methods Mol Biol ; 1061: 211-29, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23963940

RESUMEN

The specific regions on proteins which are responsible for protein-protein interaction are called interacting domains, or epitopes in case of antigen-antibody binding. These domains are one feature to characterize proteins and are important in clinical diagnostics and research. For the mapping of such domains the use of protein/peptide arrays has become popular. Regardless of which kind of array, the major requirements are a high number of candidates arranged in the array, high quality, ease of use, and cost-effectiveness. Here, the authors describe a general protocol for mapping the interacting domains of proteins demonstrated by a high affinity protein interaction, the interaction of an antibody to an antigen. The chapter describes a stepwise protocol from library production to the verification of the domain by the use of an automated cell-based polypeptide array, which comprises the named requirements of a good array.


Asunto(s)
Epítopos/análisis , Péptidos/análisis , Análisis por Matrices de Proteínas/métodos , Animales , Epítopos/inmunología , Humanos , Péptidos/inmunología
16.
ACS Chem Biol ; 8(11): 2442-51, 2013 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-23957438

RESUMEN

Modern medicine is founded on the discovery of penicillin and subsequent small molecules that inhibit bacterial peptidoglycan (PG) and cell wall synthesis. However, the discovery of new chemically and mechanistically distinct classes of PG inhibitors has become exceedingly rare, prompting speculation that intracellular enzymes involved in PG precursor synthesis are not 'druggable' targets. Here, we describe a ß-lactam potentiation screen to identify small molecules that augment the activity of ß-lactams against methicillin-resistant Staphylococcus aureus (MRSA) and mechanistically characterize a compound resulting from this screen, which we have named murgocil. We provide extensive genetic, biochemical, and structural modeling data demonstrating both in vitro and in whole cells that murgocil specifically inhibits the intracellular membrane-associated glycosyltransferase, MurG, which synthesizes the lipid II PG substrate that penicillin binding proteins (PBPs) polymerize and cross-link into the cell wall. Further, we demonstrate that the chemical synergy and cidality achieved between murgocil and the ß-lactam imipenem is mediated through MurG dependent localization of PBP2 to the division septum. Collectively, these data validate our approach to rationally identify new target-specific bioactive ß-lactam potentiation agents and demonstrate that murgocil now serves as a highly selective and potent chemical probe to assist our understanding of PG biosynthesis and cell wall biogenesis across Staphylococcal species.


Asunto(s)
Antibacterianos/farmacología , Proteínas de la Membrana Bacteriana Externa/antagonistas & inhibidores , N-Acetilglucosaminiltransferasas/antagonistas & inhibidores , Peptidoglicano Glicosiltransferasa/metabolismo , Pirazoles/farmacología , Staphylococcus aureus/efectos de los fármacos , Esteroles/farmacología , Simulación por Computador , Farmacorresistencia Bacteriana , Inhibidores Enzimáticos/farmacología , Humanos , Microscopía Fluorescente , Modelos Moleculares , Pirazoles/química , Staphylococcus aureus/enzimología , Esteroles/química
17.
Assay Drug Dev Technol ; 11(5): 333-46, 2013 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-23772554

RESUMEN

Steady improvements in proteomics present a bioinformatic challenge to retrieve, store, and process the accumulating and often redundant amount of information. In particular, a large-scale comparison and analysis of protein-protein interaction (PPI) data requires tools for data interpretation as well as validation. At this juncture, the Protein Interaction and Molecule Search (PRIMOS) platform represents a novel web portal that unifies six primary PPI databases (BIND, Biomolecular Interaction Network Database; DIP, Database of Interacting Proteins; HPRD, Human Protein Reference Database; IntAct; MINT, Molecular Interaction Database; and MIPS, Munich Information Center for Protein Sequences) into a single consistent repository, which currently includes more than 196,700 redundancy-removed PPIs. PRIMOS supports three advanced search strategies centering on disease-relevant PPIs, on inter- and intra-organismal crosstalk relations (e.g., pathogen-host interactions), and on highly connected protein nodes analysis ("hub" identification). The main novelties distinguishing PRIMOS from other secondary PPI databases are the reassessment of known PPIs, and the capacity to validate personal experimental data by our peer-reviewed, homology-based validation. This article focuses on definite PRIMOS use cases (presentation of embedded biological concepts, example applications) to demonstrate its broad functionality and practical value. PRIMOS is publicly available at http://primos.fh-hagenberg.at.


Asunto(s)
Sistemas de Administración de Bases de Datos , Bases de Datos de Proteínas , Almacenamiento y Recuperación de la Información/métodos , Internet , Mapeo de Interacción de Proteínas/métodos , Proteoma/química , Proteoma/metabolismo , Integración de Sistemas , Interfaz Usuario-Computador
18.
Assay Drug Dev Technol ; 11(4): 269-75, 2013 May.
Artículo en Inglés | MEDLINE | ID: mdl-23679850

RESUMEN

The yeast two-hybrid (Y2H) system is one of the most technically straightforward, effective, and widely used tools for the discovery of the binary peptide or protein interactions. However, its exceptional detection sensitivity poses a serious challenge for affinity ranking and hence prioritizing the resultant large number of putative interactors for follow-up analyses. To overcome this apparent bottleneck, we describe here a novel yeast growth curve-based interaction-monitoring approach that permits semiautomatic quantification, comparison, and statistically ascertained scoring of a large collection of Y2H interactions under real-time conditions. Initially, we conducted a proof-of-concept test of five literature-validated peptide-protein interactions with known affinities in the low µM range, and subsequently used the method to classify 88 novel vitamin D receptor-binding peptides derived from high-throughput screening of a highly diverse artificial peptide aptamer library. Based on our in-depth data evaluation, we conclude that real-time monitoring of clone growth as a measure of relative binding strength offers a facile, cost-effective, accurate, reproducible, and further adaptable complement to standard Y2H-derived clone management.


Asunto(s)
Ensayos Analíticos de Alto Rendimiento/métodos , Péptidos/química , Proteínas/química , Técnicas del Sistema de Dos Híbridos , Sitios de Unión , Sistemas de Computación , Unión Proteica
19.
Biomed Res Int ; 2013: 521281, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23509735

RESUMEN

Epidermolysis bullosa (EB) is a group of inherited skin disorders characterized by blistering following mechanical trauma. Chronic wounds of EB patients often lead to tumors such as squamous cell carcinoma (SCC). Early diagnosis may prevent its invasive growth--frequently the reason of premature mortality of EB-patients. Early detection of tumors is achieved by fluorescence diagnosis (FD), where photosensitizers localize selectively in tumors and fluoresce upon illumination. Excessive accumulation of photosensitizers in inflamed areas, as occasionally found at chronic wounds and tumors due to inflammatory processes, leads to false-positive results in FD. This study analyzed accumulation kinetics of the photosensitizers hypericin and endogenous protoporphyrin IX (PpIX) in different skin cell lines including the three EB subtypes under normal and proinflammatory conditions (stimulated with TNF-alpha). The aim was to assess the applicability of FD of SCC in EB. All cell lines accumulate hypericin or PpIX mostly increasing with incubation time, but with different kinetics. SCC cells of recessive dystrophic EB (RDEB) accumulate less hypericin or PpIX than nonmalignant RDEB cells. Nevertheless, tumor selectivity in vivo might be existent. Non-EB cell lines are more active concerning photosensitizer enrichment. Proinflammatory conditions of skin cell lines seem to have no major influence on photosensitizer accumulation.


Asunto(s)
Carcinoma de Células Escamosas/diagnóstico , Epidermólisis Ampollosa/diagnóstico , Colorantes Fluorescentes/farmacocinética , Microscopía Fluorescente/métodos , Fármacos Fotosensibilizantes/farmacocinética , Neoplasias Cutáneas/diagnóstico , Antracenos , Carcinoma de Células Escamosas/complicaciones , Línea Celular Tumoral , Epidermólisis Ampollosa/complicaciones , Reacciones Falso Positivas , Fibroblastos/citología , Humanos , Inflamación , Queratinocitos/citología , Perileno/análogos & derivados , Perileno/metabolismo , Perileno/farmacocinética , Perileno/farmacología , Protoporfirinas/metabolismo , Neoplasias Cutáneas/complicaciones
20.
Exp Dermatol ; 22(4): 292-4, 2013 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-23528216

RESUMEN

An important characteristic of epidermolysis bullosa simplex Dowling-Meara (EBS-DM) keratinocytes is the increased level of Jun N-terminal kinase (JNK) stress signalling, which is thought to contribute to the disease phenotype. In this work, we report on the dramatic up-regulation of cytokeratin 14 (K14) in the EBS-DM model cell line KEB7 at both the transcriptional and translational levels, which is noteworthy because KEB7 patient cells are heterozygous for a missense mutation (R125P) in K14. By performing functional assays, we show a direct link between overexpressed wild-type K14 and increased JNK signalling in healthy, immortalized keratinocytes. This observation led us to hypothesize a positive feedback model in which mutant (R125P) K14 triggers JNK signalling, leading to increased AP1-dependent expression of K14, which in turn amplifies JNK signalling further. We therefore suggest that an imbalance of cytoplasmic K14 monomers and K14 incorporated into the intermediate filament (IF) network leads to elevated stress signalling, potentially altering IF dynamics by phosphorylation, which as a side effect, weakens EBS-DM keratinocytes.


Asunto(s)
Epidermólisis Ampollosa Simple/metabolismo , Queratina-14/metabolismo , Línea Celular , Epidermólisis Ampollosa Simple/genética , Humanos , Filamentos Intermedios/metabolismo , Queratina-14/genética , Queratinocitos/metabolismo , Sistema de Señalización de MAP Quinasas , Modelos Biológicos , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Mutación Missense , Estrés Fisiológico , Factor de Transcripción AP-1/metabolismo
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